The Cambridge Structural Database (CSD) is the most complete database of organic and organometallic crystal structures available. It features a suite of sophisticated search techniques, the centerpiece of which is a structural fragment search, and it provides a variety of output formats. The CSD is useful for a variety of purposes, including checking the novelty of a prospective or actual synthetic target, comparing structural features among similar compounds, obtaining structural models for calculation or visualization, and performing statistical analyses. The CSD is copyrighted as a collection, and is owned and maintained by the Cambridge Crystallographic Data Center (CCDC).
The principal criterion for inclusion of a structure in the CSD is that it be organic or organometallic in nature. For the CSD's purposes, a structure is considered to satisfy that criterion if it contains at least one carbon -- carbon or carbon -- hydrogen bond anywhere in the structure. Of all the possible structures satisfying the CSD's inclusion criterion, the CSD includes all those that have been published (up to 3-6 months prior to the current release) as well as some structures submitted directly to the CCDC for inclusion.
CSD at Indiana University
- Environment.Deployment of the CSD at IU is coordinated by the IUMSC. For the greatest allowable accessibility, the CSD is physically located on the UITS central systems, on the research SP system. The HTML version of the CSD User's Manual is on-line at http://sp-www.iu.edu/cambridge/index.html. It is necessary to have a login account on the SP system to use the CSD; these can be requested through the UITS automated account management system, but students must be sponsored by a faculty member. The CSD utilizes an X Window interface, so it is necessary to have an X Server running on the local system from which you are working. X Servers are available for Windows, Mac OS, and all flavors and variants of UNIX. UNIX workstations, however, typically have the most robust implementations, and some (especially SGI) run X all the time.
- Configuration. The CSD relies on several environment variables to run correctly. For user convenience, two scripts are provided to set up the environment correctly: one script (/usr/local/bin/csdsetup-sh) for users of the sh shell and its derivatives, and another (/usr/local/bin/csdsetup-csh) for users of the csh shell and its derivatives. You can run the appropriate script by hand, but it may be more convenient to call it automatically from your configuration scripts. For the sh shell add the following line to the end of your .profile file:
. /usr/local/bin/csdsetup-sh (Don't forget that leading period!) For the csh shell add the following line to the end of your .login file:
source /usr/local/bin/csdsetup-csh There's nothing wrong with doing both. When either script runs it prints a message similar to the following:
Environment set up for CSD access. Remember to grant appropriate local
permissions with, e.g.,
xhost sp17.ucs.indiana.edu You may have to execute the specified xhost command on your local machine in order to permit the CSD interface to be displayed there (UNIX systems, mainly).
- Operation. To search the CSD, first connect to any SP node using telnet or ssh. Make sure that the X server is running on your local machine, then run the "quest" program on the SP. Normally quest takes one argument, a string to use as the base for all of the output file names. (E.g., if you execute "quest foo" you may get output files foo.jnl, foo.ins, foo.bib, etc..) Some introductory messages should come up in the terminal window, and eventually you get a prompt. Type "init 17" at the prompt, and tell it that yes, you do want to purge your journal. Then look for the interface to pop up in the display area of your X server.
Detailed instructions on how to use quest are beyond the scope of this document; if you need such assistance then you should consult the manual.
- For More Help. The staff of the IUMSC has extensive experience with using the CSD, and can help with many common problems. For SP-specific assistance, start with the UITS Knowledge Base. The configuration scripts and this document were prepared by John Bollinger of the IUMSC.
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